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- PDB-5vu2: Electron cryo-microscopy of "immature" Chikungunya VLP -

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Basic information

Entry
Database: PDB / ID: 5vu2
TitleElectron cryo-microscopy of "immature" Chikungunya VLP
Components
  • (E1 envelope glycoprotein) x 2
  • E2 envelope glycoprotein
  • E3 envelope glycoprotein
  • capsid proteinCapsid
KeywordsVIRUS LIKE PARTICLE / Chikungunya / virus / immature
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Togavirin / Togavirin / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus strain Senegal 37997
Chikungunya virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsRossmann, M.G. / Yap, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095366 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structural studies of Chikungunya virus maturation.
Authors: Moh Lan Yap / Thomas Klose / Akane Urakami / S Saif Hasan / Wataru Akahata / Michael G Rossmann /
Abstract: Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. ...Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here we present a cryo-EM, 6.8-Å resolution structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus have a larger radius and are less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins have less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addition, the nucleocapsid of the immature virus is more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the posttranslational processing of the spikes and nucleocapsid is necessary to produce infectious virus.
History
DepositionMay 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-8734
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)911,44424
Polymers911,44424
Non-polymers00
Water0
1
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 60


Theoretical massNumber of molelcules
Total (without water)54,686,6421440
Polymers54,686,6421440
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 5


  • icosahedral pentamer
  • 4.56 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)4,557,220120
Polymers4,557,220120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 6


  • icosahedral 23 hexamer
  • 5.47 MDa, 144 polymers
Theoretical massNumber of molelcules
Total (without water)5,468,664144
Polymers5,468,664144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
E1 envelope glycoprotein


Mass: 95538.164 Da / Num. of mol.: 8 / Fragment: UNP residues 326-1191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: A0A0H4CWF2
#2: Protein
E3 envelope glycoprotein


Mass: 6926.990 Da / Num. of mol.: 4 / Fragment: UNP residues 266-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Gene: CHIKVgp2 / Production host: Homo sapiens (human) / References: UniProt: C7S7A1, UniProt: Q5XXP3*PLUS
#3: Protein
capsid protein / Capsid


Mass: 16229.508 Da / Num. of mol.: 4 / Fragment: UNP residues 113-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus (strain 37997) / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
#4: Protein/peptide
E1 envelope glycoprotein


Mass: 4810.723 Da / Num. of mol.: 4 / Fragment: transmembrane helix (UNP residues 1203-1248)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
#5: Protein
E2 envelope glycoprotein


Mass: 8817.458 Da / Num. of mol.: 4 / Fragment: transmembrane helix (UNP residues 668-748)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chikungunya virus strain Senegal 37997 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Chikungunya virus strain Senegal 37997
Source (recombinant)Organism: Homo sapiens (human) / Cell: Human embryonic kidney / Plasmid: pUC119
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
7EMfitmodel fitting
13jspr3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72944 / Symmetry type: POINT

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